Changelog

This project adheres to Semantic Versioning and Keep a Changelog format.

[0.11.0] - 2026-02-18

New gtars features exposed in refget Python API: compute_fai, digest_sequence, and SequenceCollection now available via import refget
FHR metadata support: refget store metadata and refget store metadata-set commands for managing collection metadata
refget store pull command for fetching collections from remote servers into your local store
Seqcol CLI commands (show, compare, validate) now look up collections in the local store before querying remote servers
GA4GH compliance test suite with 65 checks covering all seqcol spec endpoints, runnable via pytest or the web UI
Web UI compliance runner with real-time streaming results, stop button, and per-test descriptions
Swagger/OpenAPI documentation for all API query parameters
gtars version displayed in service-info and frontend footer badges
Download collections in seqcol JSON format from the web UI

Fix CLI store list JSON serialization error (was returning non-serializable metadata objects)
Fix CLI store get, store remove, and store pull commands that failed to find collections
Update CLI to use iter_collections() API instead of removed collections() method

Major restructure of the package with new comprehensive CLI (refget command)
New CLI subcommands: admin, config, fasta, seqcol, and store
Implement FASTA DRS objects for serving FASTA files via GA4GH DRS endpoints
Add RefgetStore integration for local sequence storage via gtars
Refactor to isolate gtars dependency, improving import performance
Add service-info capabilities for fasta_drs and refget_store features
New integration test framework with ephemeral Docker PostgreSQL
Comprehensive CLI test suite
API compliance tests against GA4GH seqcol specification
Fix endpoint path: /list/collection (was /list/collections in client)
New browser-based /digest feature for computing seqcol digests from FASTA files entirely client-side using @databio/gtars WASM module

performance fix for calculating jaccard similarties
add human_readable_name list as an attribute to SequenceCollection for displaying similarity results
adding SequenceCollections via PEP will now add associated sample_name as a human_readable_name
add wrapper for gtars RefgetStore so it can be called directly from refget

adds API endpoints for jaccard similarity calculations
some refactoring for newest gtars, v0.3.0
add class method from_PySequenceCollection for creating SequenceCollection from a gtars-created SequenceCollection
adds Similarity UI to frontend

updated add method to use boolean for updating SequenceCollection if already exists

Complete rewrite of the clients and agents.
New SequenceAgent class allows using the RefgetDBAgent class to store sequences. This is meant for testing purposes.
Completely refactored Clients work adds mature SequenceClient and SequenceCollectionClient classes.
Fix issues with rust digest calculations to improve flexibilty, using latest update to gtars interface.
Updates to latest ga4gh paging guidance
Add a beta CLI with digest-fasta and add-fasta functionality.
Remove some old stuff based on henge backend

Major revamp to RefGetClient object, which now works with either sequences or seqcol servers, and can handle any of the seqcol API endpoints.
Better integration of rust digest calculations built on gtars
switch back-end to use JSON instead of str
implement name_length_pairs and sorted_sequences attrs
improve some SeqCol object representations

Change paging style of list endpoints to match latest GA4GH pagination guide
Implement new /list/attribute endpoint on back-end, and add to demo
Update endpoint paths slightly after discussion for the /list and /attribute endpoints
Remove some of the duplicate endpoints to solidify to one API

Beta version for testing